嗎 builds a yes-no question from a flat statement (你是學生嗎?). 呢2 attaches to a question that is already a question — the wh-word does the asking, 呢 only softens it. The two never co-occur.
呢1 drops the predicate and reuses the one just stated (……,你呢?). 呢2 keeps the full question intact, wh-word and all, and lingers on it.
你是學生呢? → 你是學生嗎? (no wh-word, so a yes-no question takes 嗎, not 呢2)
你什麼時候可以開始工作嗎呢? → 你什麼時候可以開始工作呢?
什麼時候呢你可以開始工作? → 你什麼時候可以開始工作呢? (呢 closes the sentence; it never sits mid-clause)
English softens a wh-question with extra words or a falling tone ("so when can you start?"). Mandarin leaves the question untouched and adds 呢 at the tail; there is no separate word to translate it as.